A citation-based method for searching scientific literature

Michael H Kagey, Jamie J Newman, Steve Bilodeau, Ye Zhan, David A Orlando, Nynke L van Berkum, Christopher C Ebmeier, Jesse Goossens, Peter B Rahl, Stuart S Levine, Dylan J Taatjes, Job Dekker, Richard A Young. Nature 2010
Times Cited: 1294







List of co-cited articles
1445 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Master transcription factors and mediator establish super-enhancers at key cell identity genes.
Warren A Whyte, David A Orlando, Denes Hnisz, Brian J Abraham, Charles Y Lin, Michael H Kagey, Peter B Rahl, Tong Ihn Lee, Richard A Young. Cell 2013
35

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Suhas S P Rao, Miriam H Huntley, Neva C Durand, Elena K Stamenova, Ivan D Bochkov, James T Robinson, Adrian L Sanborn, Ido Machol, Arina D Omer, Eric S Lander,[...]. Cell 2014
35

Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Jesse R Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S Liu, Bing Ren. Nature 2012
31

Cohesin Loss Eliminates All Loop Domains.
Suhas S P Rao, Su-Chen Huang, Brian Glenn St Hilaire, Jesse M Engreitz, Elizabeth M Perez, Kyong-Rim Kieffer-Kwon, Adrian L Sanborn, Sarah E Johnstone, Gavin D Bascom, Ivan D Bochkov,[...]. Cell 2017
748
30

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner,[...]. Science 2009
25

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.
Elphège P Nora, Anton Goloborodko, Anne-Laure Valton, Johan H Gibcus, Alec Uebersohn, Nezar Abdennur, Job Dekker, Leonid A Mirny, Benoit G Bruneau. Cell 2017
706
24

Human cohesin compacts DNA by loop extrusion.
Yoori Kim, Zhubing Shi, Hongshan Zhang, Ilya J Finkelstein, Hongtao Yu. Science 2019
229
21

DNA loop extrusion by human cohesin.
Iain F Davidson, Benedikt Bauer, Daniela Goetz, Wen Tang, Gordana Wutz, Jan-Michael Peters. Science 2019
256
21

Formation of Chromosomal Domains by Loop Extrusion.
Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny. Cell Rep 2016
795
21

Super-enhancers in the control of cell identity and disease.
Denes Hnisz, Brian J Abraham, Tong Ihn Lee, Ashley Lau, Violaine Saint-André, Alla A Sigova, Heather A Hoke, Richard A Young. Cell 2013
20

Two independent modes of chromatin organization revealed by cohesin removal.
Wibke Schwarzer, Nezar Abdennur, Anton Goloborodko, Aleksandra Pekowska, Geoffrey Fudenberg, Yann Loe-Mie, Nuno A Fonseca, Wolfgang Huber, Christian H Haering, Leonid Mirny,[...]. Nature 2017
484
20

Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes.
Jill M Dowen, Zi Peng Fan, Denes Hnisz, Gang Ren, Brian J Abraham, Lyndon N Zhang, Abraham S Weintraub, Jurian Schujiers, Tong Ihn Lee, Keji Zhao,[...]. Cell 2014
538
18

Coactivator condensation at super-enhancers links phase separation and gene control.
Benjamin R Sabari, Alessandra Dall'Agnese, Ann Boija, Isaac A Klein, Eliot L Coffey, Krishna Shrinivas, Brian J Abraham, Nancy M Hannett, Alicia V Zamudio, John C Manteiga,[...]. Science 2018
853
18

The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension.
Judith H I Haarhuis, Robin H van der Weide, Vincent A Blomen, J Omar Yáñez-Cuna, Mario Amendola, Marjon S van Ruiten, Peter H L Krijger, Hans Teunissen, René H Medema, Bas van Steensel,[...]. Cell 2017
345
18

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates.
Won-Ki Cho, Jan-Hendrik Spille, Micca Hecht, Choongman Lee, Charles Li, Valentin Grube, Ibrahim I Cisse. Science 2018
515
17

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers.
Laila El Khattabi, Haiyan Zhao, Jens Kalchschmidt, Natalie Young, Seolkyoung Jung, Peter Van Blerkom, Philippe Kieffer-Kwon, Kyong-Rim Kieffer-Kwon, Solji Park, Xiang Wang,[...]. Cell 2019
80
21

Spatial partitioning of the regulatory landscape of the X-inactivation centre.
Elphège P Nora, Bryan R Lajoie, Edda G Schulz, Luca Giorgetti, Ikuhiro Okamoto, Nicolas Servant, Tristan Piolot, Nynke L van Berkum, Johannes Meisig, John Sedat,[...]. Nature 2012
16

Organizational principles of 3D genome architecture.
M Jordan Rowley, Victor G Corces. Nat Rev Genet 2018
395
16

Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
15

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
15

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains.
Ann Boija, Isaac A Klein, Benjamin R Sabari, Alessandra Dall'Agnese, Eliot L Coffey, Alicia V Zamudio, Charles H Li, Krishna Shrinivas, John C Manteiga, Nancy M Hannett,[...]. Cell 2018
565
15

Cohesin mediates transcriptional insulation by CCCTC-binding factor.
Kerstin S Wendt, Keisuke Yoshida, Takehiko Itoh, Masashige Bando, Birgit Koch, Erika Schirghuber, Shuichi Tsutsumi, Genta Nagae, Ko Ishihara, Tsuyoshi Mishiro,[...]. Nature 2008
829
15

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.
Adrian L Sanborn, Suhas S P Rao, Su-Chen Huang, Neva C Durand, Miriam H Huntley, Andrew I Jewett, Ivan D Bochkov, Dharmaraj Chinnappan, Ashok Cutkosky, Jian Li,[...]. Proc Natl Acad Sci U S A 2015
814
15

A Phase Separation Model for Transcriptional Control.
Denes Hnisz, Krishna Shrinivas, Richard A Young, Arup K Chakraborty, Phillip A Sharp. Cell 2017
746
14

HiChIP: efficient and sensitive analysis of protein-directed genome architecture.
Maxwell R Mumbach, Adam J Rubin, Ryan A Flynn, Chao Dai, Paul A Khavari, William J Greenleaf, Howard Y Chang. Nat Methods 2016
451
14

Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions.
Darío G Lupiáñez, Katerina Kraft, Verena Heinrich, Peter Krawitz, Francesco Brancati, Eva Klopocki, Denise Horn, Hülya Kayserili, John M Opitz, Renata Laxova,[...]. Cell 2015
14

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation.
Sergi Cuartero, Felix D Weiss, Gopuraja Dharmalingam, Ya Guo, Elizabeth Ing-Simmons, Silvia Masella, Irene Robles-Rebollo, Xiaolin Xiao, Yi-Fang Wang, Iros Barozzi,[...]. Nat Immunol 2018
100
14


Histone H3K27ac separates active from poised enhancers and predicts developmental state.
Menno P Creyghton, Albert W Cheng, G Grant Welstead, Tristan Kooistra, Bryce W Carey, Eveline J Steine, Jacob Hanna, Michael A Lodato, Garrett M Frampton, Phillip A Sharp,[...]. Proc Natl Acad Sci U S A 2010
13

Imaging dynamic and selective low-complexity domain interactions that control gene transcription.
Shasha Chong, Claire Dugast-Darzacq, Zhe Liu, Peng Dong, Gina M Dailey, Claudia Cattoglio, Alec Heckert, Sambashiva Banala, Luke Lavis, Xavier Darzacq,[...]. Science 2018
391
13

An oestrogen-receptor-alpha-bound human chromatin interactome.
Melissa J Fullwood, Mei Hui Liu, You Fu Pan, Jun Liu, Han Xu, Yusoff Bin Mohamed, Yuriy L Orlov, Stoyan Velkov, Andrea Ho, Poh Huay Mei,[...]. Nature 2009
13

Architectural protein subclasses shape 3D organization of genomes during lineage commitment.
Jennifer E Phillips-Cremins, Michael E G Sauria, Amartya Sanyal, Tatiana I Gerasimova, Bryan R Lajoie, Joshua S K Bell, Chin-Tong Ong, Tracy A Hookway, Changying Guo, Yuhua Sun,[...]. Cell 2013
748
13

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
12

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
12

Widespread transcription at neuronal activity-regulated enhancers.
Tae-Kyung Kim, Martin Hemberg, Jesse M Gray, Allen M Costa, Daniel M Bear, Jing Wu, David A Harmin, Mike Laptewicz, Kellie Barbara-Haley, Scott Kuersten,[...]. Nature 2010
12

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription.
Fan Lai, Ulf A Orom, Matteo Cesaroni, Malte Beringer, Dylan J Taatjes, Gerd A Blobel, Ramin Shiekhattar. Nature 2013
586
12

YY1 Is a Structural Regulator of Enhancer-Promoter Loops.
Abraham S Weintraub, Charles H Li, Alicia V Zamudio, Alla A Sigova, Nancy M Hannett, Daniel S Day, Brian J Abraham, Malkiel A Cohen, Behnam Nabet, Dennis L Buckley,[...]. Cell 2017
380
12

Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.
Gordana Wutz, Csilla Várnai, Kota Nagasaka, David A Cisneros, Roman R Stocsits, Wen Tang, Stefan Schoenfelder, Gregor Jessberger, Matthias Muhar, M Julius Hossain,[...]. EMBO J 2017
314
12

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells.
Jessica Zuin, Jesse R Dixon, Michael I J A van der Reijden, Zhen Ye, Petros Kolovos, Rutger W W Brouwer, Mariëtte P C van de Corput, Harmen J G van de Werken, Tobias A Knoch, Wilfred F J van IJcken,[...]. Proc Natl Acad Sci U S A 2014
489
12

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
11

Selective inhibition of tumor oncogenes by disruption of super-enhancers.
Jakob Lovén, Heather A Hoke, Charles Y Lin, Ashley Lau, David A Orlando, Christopher R Vakoc, James E Bradner, Tong Ihn Lee, Richard A Young. Cell 2013
11

An atlas of active enhancers across human cell types and tissues.
Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki,[...]. Nature 2014
11

Long-range enhancer-promoter contacts in gene expression control.
Stefan Schoenfelder, Peter Fraser. Nat Rev Genet 2019
319
11

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function.
Ya Guo, Quan Xu, Daniele Canzio, Jia Shou, Jinhuan Li, David U Gorkin, Inkyung Jung, Haiyang Wu, Yanan Zhai, Yuanxiao Tang,[...]. Cell 2015
519
11

Developmental enhancers and chromosome topology.
Eileen E M Furlong, Michael Levine. Science 2018
205
11

deepTools2: a next generation web server for deep-sequencing data analysis.
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke. Nucleic Acids Res 2016
11

Chromatin architecture reorganization during stem cell differentiation.
Jesse R Dixon, Inkyung Jung, Siddarth Selvaraj, Yin Shen, Jessica E Antosiewicz-Bourget, Ah Young Lee, Zhen Ye, Audrey Kim, Nisha Rajagopal, Wei Xie,[...]. Nature 2015
834
10


A unique chromatin signature uncovers early developmental enhancers in humans.
Alvaro Rada-Iglesias, Ruchi Bajpai, Tomek Swigut, Samantha A Brugmann, Ryan A Flynn, Joanna Wysocka. Nature 2011
10


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.